Regarding your questions, I think you should wear it until your own odor becomes the primary scent . Unless the leather has a sour smell coming from the lining then just throw it away. Not worth it bro

I recently procured a Margiela 5zip leather circa year 2000 or so. Problem is that is has that "old clothes - Salvation Army" smell. Any tips on how to get that smell out without damaging the leather?

Hang outside and air it out, maybe febreeze the inner lining. just make sure that its not a humid/damp day. That should remove some of the smell a little. Also ask a local cobbler they know their leathers .

Try putting in plastic dry cleaning bag taped shut with baking soda at bottom (on a hanger obviously without touching the stuff at the bottom). You could also substitute with charcoal or coffee grounds in a pinch (will smell like coffee though). That's my standard solution to cigarette smell on clothes.